Gene body methylation regulates gene expression and mediates phenotypic diversity in natural Arabidopsis populations
Z. Shahzad, E. Hollwey, J.D. Moore, J. Choi, G. Cassin-Ross, H. Rouached, M.R. Robinson, D. Zilberman, Nature Plants 11 (2025) 2084–2099.

Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana
V.K. Bett, M.S. Trejo Arellano, B. Vicoso, Molecular Biology and Evolution 42 (2025).

Concepts, mechanisms and implications of long-term epigenetic inheritance
E. Hollwey, A. Briffa, M. Howard, D. Zilberman, Current Opinion in Genetics and Development 81 (2023).

Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations
A. Briffa, E. Hollwey, Z. Shahzad, J.D. Moore, D.B. Lyons, M. Howard, D. Zilberman, Cell Systems 14 (2023) 953–967.

Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons
D.B. Lyons, A. Briffa, S. He, J. Choi, E. Hollwey, J. Colicchio, I. Anderson, X. Feng, M. Howard, D. Zilberman, Cell Reports 42 (2023).

Histone  prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin
J. Choi, D.B. Lyons, D. Zilberman, ELife 10 (2021).

Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting
J.A. Rodrigues, P.-H. Hsieh, D. Ruan, T. Nishimura, M.K. Sharma, R. Sharma, X. Ye, N.D. Nguyen, S. Nijjar, P.C. Ronald, R.L. Fischer, D. Zilberman, Proceedings of the National Academy of Sciences of the United States of America 118 (2021).

DNA methylation and histone  jointly repress transposable elements and aberrant intragenic transcripts
J. Choi, D.B. Lyons, M.Y. Kim, J.D. Moore, D. Zilberman, Molecular Cell 77 (2020) 310–323.e7.

DNA demethylation by ROa in rice vegetative cells promotes methylation in sperm
M.Y. Kim, A. Ono, S. Scholten, T. Kinoshita, D. Zilberman, T. Okamoto, R.L. Fischer, Proceedings of the National Academy of Sciences 116 (2019) 9652–9657.

DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development
K.D. Harris, J.P.B. Lloyd, K. Domb, D. Zilberman, A. Zemach, Epigenetics and Chromatin 12 (2019).

FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis
J.M. Frost, M.Y. Kim, G.T. Park, P.-H. Hsieh, M. Nakamura, S.J.H. Lin, H. Yoo, J. Choi, Y. Ikeda, T. Kinoshita, Y. Choi, D. Zilberman, R.L. Fischer, Proceedings of the National Academy of Sciences 115 (2018) 20–29.

DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes
D.B. Lyons, D. Zilberman, ELife 6 (2017).

An evolutionary case for functional gene body methylation in plants and animals
D. Zilberman, Genome Biology 18 (2017).

Mechanism for DNA transposons to generate introns on genomic scales
J.T. Huff, D. Zilberman, S.W. Roy, Nature 538 (2016) 533–536.

Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues
P.-H. Hsieh, S. He, T. Buttress, H. Gao, M. Couchman, R.L. Fischer, D. Zilberman, X. Feng, Proceedings of the National Academy of Sciences 113 (2016) 15132–15137.

DNA demethylation is initiated in the central cells of Arabidopsis and rice
K. Park, M.Y. Kim, M. Vickers, J.-S. Park, Y. Hyun, T. Okamoto, D. Zilberman, R.L. Fischer, X. Feng, Y. Choi, S. Scholten, Proceedings of the National Academy of Sciences 113 (2016) 15138–15143.

Evolution and function of genomic imprinting in plants
J.A. Rodrigues, D. Zilberman, Genes and Development 29 (2015) 2517–2531.

Dnm-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes
J.T. Huff, D. Zilberman, Cell 156 (2014) 1286–1297.

The AAA-ATPase molecular chaperone Cd/ disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes
Z. Mérai, N. Chumak, M. García-Aguilar, T.-F. Hsieh, T. Nishimura, V.K. Schoft, J. Bindics, L. alusarz, S. Arnoux, S. Opravil, K. Mechtler, D. Zilberman, R.L. Fischer, H. Tamaru, Proceedings of the National Academy of Sciences 111 (2014) 16166–16171.

DNA methylation as a system of plant genomic immunity
M.Y. Kim, D. Zilberman, Trends in Plant Science 19 (2014) 320–326.